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2 Answers
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In your case, it can be simply an instance of personification. That is, metaphorically handling an inanimate thing as if it were animate. That is easy to imagine with 'doll'. If that is the case, then this is not an exception but is simply a rhethoric.

A case where an inanimate thing can take いる is when that thing is inherently mobile, and is used within the context as such. For example, if you are looking at a time table, and found a train that you can take, then you can say

電車がある

but if you were running into the station to catch a train that may have left already, but you made to it in the last moment and there is a train in front of you, then you can say

電車がいる

On the other hand, when you are talking about an existence of an animate thing, and that is an ordinary scene, you can use it with ある

昔、おじいさんとおばあさんがあった
昔、おじいさんとおばあさんがいた

When you are talking about possession by nature, then you can use an animate thing with ある.

@Tsuyoshi_Ito The original form in folk tales is like that. Recently published books sometimes use いる because they have in mind a prescriptive rule that ある is used only for inanimates, which does not reflect the reality. You might have been affeced by this. This kind of thing is called hypercorrection in linguistics.
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user458Jul 27 '11 at 14:24

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Thanks! I thought that the usual phrase is おじいさんとおばあさんがおりました, but I found examples with ありました in Daijirin and Daijisen.
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Tsuyoshi ItoJul 27 '11 at 17:50

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@sawa, I don't think that's hypercorrection. It is hypercorrection if somebody expresses something in a non-standard way because they think it is more correct than what they consider natural. But: 1. "おじいさんとおばあさんがいた" is hardly non-standard, 2. They might have changed the wording, not because they thought the original wrong, but because they found it unnatural. Regardless of what used to be/is correct, many native speakers now find ある with animate things unnatural.
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dainichiFeb 13 '13 at 7:11